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I think my site has 3000+ links but only 500 seem to show, it's so confusing and annoying.

The main reason for 301s is so you dont lose traffic as SERPS sometimes dont update for a while. It carrys your Link Juice to the URL you re-direct it to which can improve your SERPS so you don't have to start your SEO from scratch. So it is quite important if you've done backlinking etc, if it's just a basic page I would still 301 it to keep Google happy.

I'm no expert, i'm sure someone will give you a more detailed answer.

I'm an x-cart user, CDSEO is a must; period.

On my Ecommerce i've just added it in robots.txt

You should be able to do something similar. Below is what I have but I use x-Cart as my ecommerce site.

User-agent: *
Disallow: /printable=Y
Disallow: /js=
Disallow: /sort=
Disallow: /sort_direction=
Disallow: /product.php
Disallow: /home.php?cat=*
Disallow: /catalog/
Disallow: /search.php
Disallow: /cart.php
Disallow: /help.php
Disallow: /giftcert.php
Disallow: /product.php
Disallow: /orders.php
Disallow: /register.php
Disallow: /icon.php
Disallow: /image.php
Disallow: /error_message.php
Disallow: /offers.php
Disallow: /product_image.php
Sitemap: http://www.domainurlhere.co.uk/sitemap.xml